Mercurial > repos > iuc > dram_strainer

annotate macros.xml @ 2:9c8f2cfb70ba draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit a5e28ac40a63a269100ddec5629aee5256ce00ef
author iuc
date Fri, 09 Feb 2024 21:35:54 +0000
parents 684676cd6512
children f081f73cc0be
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1 <macros>
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2 <token name="@TOOL_VERSION@">1.3.5</token>
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3 <!-- token name="@VERSION_SUFFIX@">0</token -->
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4 <token name="@PROFILE@">20.09</token>
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5 <xml name="bio_tools">
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6 <xrefs>
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7 <xref type="bio.tools">dram</xref>
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8 </xrefs>
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9 </xml>
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10 <xml name="requirements">
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11 <requirements>
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12 <requirement type="package" version="@TOOL_VERSION@">dram</requirement>
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13 </requirements>
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14 </xml>
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15 <xml name="stdio">
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16 <stdio>
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17 <regex match="FileNotFoundError" source="stderr" level="fatal"/>
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18 <regex match="returned non-zero exit status" source="stdout" level="fatal"/>
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19 <regex match="returned non-zero exit status" source="stderr" level="fatal"/>
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20 <regex match="Invalid file path or buffer object type" source="stderr" level="fatal"/>
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21 <exit_code range="1:" level="fatal"/>
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22 </stdio>
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23 </xml>
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24 <xml name="categories_param">
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25 <param argument="--categories" type="text" value="" label="Distillate categories" help="Optional, leave blank to ignore">
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26 <expand macro="sanitizer"/>
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27 </param>
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28 </xml>
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29 <xml name="custom_distillate_param">
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30 <param argument="--custom_distillate" type="data" format="tabular" optional="true" label="File containing a custom distillate form" help="Optional, leave blank to ignore"/>
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31 </xml>
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32 <xml name="genes_param">
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33 <param argument="--genes" type="text" value="" label="Space-separated list of genes to keep" help="Optional, leave blank to ignore">
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34 <expand macro="sanitizer"/>
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35 </param>
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36 </xml>
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37 <xml name="identifiers_param">
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38 <param argument="--identifiers" type="text" value="" label="Database identifiers" help="Optional, leave blank to ignore">
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39 <expand macro="sanitizer"/>
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40 </param>
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41 </xml>
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42 <xml name="input_file_param">
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43 <param argument="--input_file" type="data" format="tabular" label="Annotations file" help="Produced by the DRAM annotate tool"/>
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44 </xml>
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45 <xml name="sanitizer">
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46 <sanitizer>
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47 <valid initial="string.printable">
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48 <remove value="&apos;"/>
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49 </valid>
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50 <mapping initial="none">
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51 <add source="&apos;" target="__sq__"/>
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52 </mapping>
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53 </sanitizer>
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54 </xml>
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55 <token name="@WHATITDOESHEADER@">DRAM (Distilled and Refined Annotation of Metabolism) is a tool for annotating metagenomic assembled genomes and VirSorter identified viral contigs. DRAM annotates MAGs and viral contigs using UniRef90, PFAM, dbCAN, RefSeq viral, VOGDB and the MEROPS peptidase database.</token>
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56 <token name="@CUSTOMDISTILLATEFILES@">**Using Custom Distillate files**
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57
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58 The custom distillate sheet must be a tabular file with all the columns specified below. This sheet is an extension
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59 of the genome_summary_form.tsv file that is installed with the dram databases and which is one of several key data files
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60 that characterizes the distillate. The genome_summary_form.tsv file is available for viewing here
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61 https://github.com/WrightonLabCSU/DRAM/blob/master/data/genome_summary_form.tsv. The custom distillate sheet must
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62 contain the following columns.
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63
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64 * gene_id: the KO ids of the genes in which you are interested
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65 * gene_description: descriptions of the geans
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66 * module: the name of your module that you are adding
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67 * sheet: the name you would like on the excel sheet in which your results appear
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68 * header: the header that will appear in the dram metabolism summary
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69 * subheader: the sub-header that will appear in the metabolism summary</token>
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70 <token name="@WHATITDOESFOOTER@">More information about DRAM can be found here https://github.com/shafferm/DRAM/wiki.</token>
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71 <xml name="citations">
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72 <citations>
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73 <citation type="doi">10.1186/s13104-016-1900-2</citation>
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74 </citations>
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75 </xml>
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76 </macros>
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77